1. The flag is waving way up high.

(What is the meaning of 'way up' in this sentence?)

2. Lunch for free!
3. Lunch is for free!
4. We have lunch for free!
5. You can have lunch for free!

(What does #2 mean? Does #2 mean #3, #4, or #5?)

1. The phrase "way up" is a colloquial substitute for "very," that's all.

2 means you don't have to pay for lunch.

3, 4, and 5 are about the same as 2. Using "for" in these sentences seems awkward to me, but these sentences would be worse without it, I guess! It just seems to be an unnecessary word.